Minute Torsional Reorganization Elicited Large Visible Range Fluorescence Gain in Terphenyl Derived Crystals

Understanding the variations in the solid-state optical signals of organic semiconductor materials upon subtle structural rearrangement or intermolecular interactions would help to extract the best performance in their electro-optic devices....

Structural basis for broad anti-phage immunity by DISARM

In the evolutionary arms race against phage, bacteria have assembled a diverse arsenal of antiviral immune strategies. While the recently discovered DISARM (Defense Island System Associated with Restriction-Modification) systems can provide protection against a wide range of phage, the molecular mechanisms that underpin broad antiviral targeting but avoiding autoimmunity remain enigmatic. Here, we report cryo-EM structures of the core DISARM complex, DrmAB, both alone and in complex with an unmethylated phage DNA mimetic. These structures reveal that DrmAB core complex is autoinhibited by a trigger loop (TL) within DrmA and binding to DNA substrates containing a 5' overhang dislodges the TL, initiating a long-range structural rearrangement for DrmAB activation. Together with structure-guided in vivo studies, our work provides insights into the mechanism of phage DNA recognition and specific activation of this widespread antiviral defense system.

Structural and Optical Modifications in the BaO-ZnO-LiF-B2O3-Yb2O3 Glass System after γ-Irradiation

A Yb3+-doped borate glass system was examined for the structural and optical modifications after γ-irradiation. Among the studied 10BaO-20ZnO-20LiF-(50-x)B2O3-xYb2O3 (x = 0.1, 0.5, 0.7, and 1.0 mol%) glasses, the 10BaO-20ZnO-20LiF-49.9B2O3-0.1Yb2O3 glass showed the highest thermoluminescence intensity, trap density, and trap depth. The glass was irradiated with the optimum γ-dose of 1 kGy towards the analysis of radiation-induced defects. The amorphous nature was preserved before and after irradiation. The glass density slightly increased after irradiation. The structural rearrangement was evident from the Fourier transform infrared spectroscopy by the appearance and disappearance of some bonds after γ-irradiation. The transformation of [BO4] units into [BO3] units and non-bridging oxygens was deduced. The color of the glass darkened after irradiation and the optical absorption intensity enhanced between 250 and 700 nm. The optical bandgap reduced and Urbach energy increased upon γ-dose exposure. The electron spin resonance of the irradiated glass exhibited two signals at g = 2.0167 and g = 1.9938, corresponding to the non-bridging oxygen hole center and Boron E’-center, respectively.

Cold Denaturation of Proteins in the Absence of Solvent

The effect of temperature on the stability of proteins is well explored for high temperatures, but harder to track below the freezing point of water. This challenge is met with the use of variable temperature ion mobility mass spectrometry (VT IM-MS), which allows the structure of isolated, solvent free molecules to be measured at sub ambient temperatures in the form of their collision cross section (CCS). Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies over a temperature range from 295 to 165 K. For each we observe a large increase in the magnitude of the CCS at 250K (-20 °C) substantially above that predicted. This loss of structure in the absence of bulk solvent is attributed to a change in the strength of stabilizing intermolecular interactions, causing rearrangement. At 190 K (-80 °C) the CCS distribution narrows which we attribute to better resolution. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the gas phase native fold supporting this practice in vitro. Comparing the data for each isotype suggests that the disulfide bridging influences thermal structural rearrangement and taken together we show that this method provides unique insights to the phenomenon of cold denaturation.

Phosphorylation-dependent BRD4 dimerization and implications for therapeutic inhibition of BET family proteins

Bromodomain-containing protein 4 (BRD4) is an epigenetic reader and oncology drug target that regulates gene transcription through binding to acetylated chromatin via bromodomains. Phosphorylation by casein kinase II (CK2) regulates BRD4 function, is necessary for active transcription and is involved in resistance to BRD4 drug inhibition in triple-negative breast cancer. Here, we provide the first biophysical analysis of BRD4 phospho-regulation. Using integrative structural biology, we show that phosphorylation by CK2 modulates the dimerization of human BRD4. We identify two conserved regions, a coiled-coil motif and the Basic-residue enriched Interaction Domain (BID), essential for the BRD4 structural rearrangement, which we term the phosphorylation-dependent dimerization domain (PDD). Finally, we demonstrate that bivalent inhibitors induce a conformational change within BRD4 dimers in vitro and in cancer cells. Our results enable the proposal of a model for BRD4 activation critical for the characterization of its protein-protein interaction network and for the development of more specific therapeutics.

Anaerobic Microscopic Analysis of Ferrous Saponite and Its Sensitivity to Oxidation by Earth’s Air: Lessons Learned for Analysis of Returned Samples from Mars and Carbonaceous Asteroids

Ferrous saponite is a secondary mineral that can be used to reveal the redox state of past aqueous environments on Mars. In mineralogical analyses for ferrous saponite formed in laboratory simulations or contained in future returned samples from Mars, its oxidation by the Earth’s air could be problematic due to the high redox sensitivity. Here, we performed micro X-ray diffraction and scanning transmission X-ray microscopy analyses for a single particle of synthesized ferrous saponite without any exposure to air. The sample was reanalyzed after air exposure for 10–18 h to assess the adequacy of our anoxic preparation/measurement methods and the impacts of air on the sample. We found that the crystal structures agreed with ferrous saponite, both before and after air exposure; however, ferrous iron in saponite was partially oxidized, at least until 0.1–1 μm from the surface, after air exposure at the submicron scale, forming micro-vein-like Fe(III)-rich features. Together with our results of infrared spectroscopy of ferrous saponite, we showed that oxidation of octahedral iron occurred rapidly and heterogeneously, even in a short time of air exposure without any structural rearrangement. Since ferrous saponite is expected to exist on carbonaceous asteroids and icy dwarf planets, our methodology is also applicable to mineralogical studies of samples returned from these bodies.

Diagnostic Utility of Multimodal Genomic Profiling for Molecular Classification and MRD Assessment in Adult B-Cell Acute Lymphoblastic Leukemia

Genomic markers define molecular subtypes and measurable residual disease (MRD) targets in B-cell acute lymphoblastic leukemia/lymphoma (B-ALL) and are essential determinants of treatment. Current diagnostic approaches typically involve serial multi-step testing utilizing conventional cytogenetics (CC)/FISH and molecular genetic (RT-qPCR, MLPA, clonality PCR, NGS panel) techniques which are time and sample consuming and ultimately may not adequately identify genomically complex B-ALL subtypes. In contrast, single-step comprehensive genomic profiling by whole genome and whole transcriptome sequencing (WGS/WTS) may be more efficient for the molecular classification of established and newly described entities which are of increasing therapeutic relevance. We have instituted a multimodal platform for molecular testing in B-ALL performing WGS/WTS in parallel with deep NGS-based immunoglobulin (IG) rearrangement MRD and exploratory DNA-breakpoint based MRD assays. We aimed to determine the utility of this approach for subtype classification compared to a standard-of-care diagnostic approach of CC/FISH testing. Forty-two consecutive adult patients underwent both standard-of-care diagnostic testing and WGS/WTS. 20/42 (48%) patients had an abnormal CC/FISH result supporting classification into recognized molecular subgroups. WGS/WTS assessment incorporating somatic coding and non-coding mutations, structural variants, fusions, copy number abnormalities and gene expression subtype prediction (ALLSorts, https://github.com/Oshlack/ALLSorts) was performed with concordant results in all 20 patients. 16/22 patients that were unclassified by CC/FISH were successfully reclassified by WGS/WTS including subtypes enriched for cryptic rearrangements (Ph-like, DUX4, MEF2D) and groups characterized by heterogeneous genomic alterations or a distinctive gene expression signature (PAX5alt, ZEB2/CEBP). A low hypodiploid karyotype was observed in two cases with an apparently normal karyotype by CC. The six patients who remained without a subtype defining driver genetic alteration after comprehensive testing frequently harbored novel IGH translocations or a Ph-like expression signature but without a described fusion. In order to understand the relative contribution from WGS versus WTS, analysis of 36 patients was performed using a truth classification. WGS and WTS produced equivalent classifications for 22 cases. Two cases were based solely on WGS findings (iAMP21 and ZEB2/CEBP) and three cases were based solely on WTS findings (DUX4). Importantly the combination of both WGS and WTS was critical to correctly classify nine cases (Ph-like and PAX5alt). MRD was assessed by a sensitive NGS assay to IG rearrangements (Adaptive Biotechnologies) and by quantitative probe-based droplet digital PCR (ddPCR) assays designed to structural rearrangement DNA breakpoints from genome data (analytical sensitivity 10 -4). Patient-specific ddPCR assays were designed to eight structural variants (KMT2A and IGH translocations, and IKZF1 deletions) in seven patients and assessed in 36 remission samples with parallel testing by multiparametric flow cytometry (MFC). Concordant MFC and ddPCR was observed in 30/36 samples (19 MRD pos, 11 MRD neg). Discordances included two MRD pos by MFC-only and four MRD pos by ddPCR-only; the latter often occurring in the setting of antigen directed therapy or in ALL with a less informative immunophenotype, demonstrating the additional utility of non-MFC based MRD assessment in specific clinical settings. 27/42 patients in our cohort had ≥1 genomic structural rearrangement identified by WGS that could be used for patient-specific MRD monitoring to complement existing MRD assessment. In conclusion WGS/WTS provided a molecular subtype classification in 86% of our cohort compared to 48% by standard-of-care diagnostic testing highlighting that CC/FISH alone is inadequate for contemporary molecular classification of B-ALL, which may have implications for treatment decisions. Importantly, the combination of WGS and WTS was superior to WGS-only or WTS-only for correct molecular subtype assignment. This approach has the potential to improve risk assessment in adult B-ALL and the routine feasibility, improvement in clinical outcomes and health economic impact warrant further assessment. Disclosures Bajel: Abbvie, Amgen, Novartis, Pfizer: Honoraria; Amgen: Speakers Bureau. Dickinson: Janssen: Consultancy, Honoraria; Amgen: Honoraria; Celgene: Research Funding; Gilead Sciences: Consultancy, Honoraria, Speakers Bureau; MSD: Consultancy, Honoraria, Research Funding, Speakers Bureau; Takeda: Research Funding; Bristol-Myers Squibb: Consultancy, Honoraria; Roche: Consultancy, Honoraria, Other: travel, accommodation, expenses, Research Funding, Speakers Bureau; Novartis: Consultancy, Honoraria, Research Funding, Speakers Bureau. Tiong: Servier: Consultancy, Speakers Bureau; Amgen: Speakers Bureau; Pfizer: Consultancy.

DIGEST Scale Predictis More Quality of Life Than PAS: the Residue Influence on Supracricoid Laryngectomy

Introduction Supracricoid laryngectomy (SCL CHEP) removes ∼ 70% of the larynx, resulting in structural rearrangement and modification of the swallowing mechanism, promoting chronic dysphagia. One of the consequences of this new physiology is the formation of pharyngeal residues that can increase the possibility of aspiration. The formation of residues after SCL CHEP, its functional consequences, and its influence on quality of life (QOL) is still poorly described in the literature. Objective To investigate and compare the association between self-reported QoL and objective assessments of swallowing function in patients undergoing SCL CHEP. Methods A cross-sectional study was performed from 2018 to 2020 in a reference service for head and neck surgery in Brazil. A total of 860 swallowing videofluoroscopy images were evaluated using the Penetration and Aspiration Scale (PAS) and Dynamic Imaging Grade of Swallowing Toxicity (DIGEST). Results In a group of 86 patients, there was a significant relationship between oncological staging and the global (p < 0.001) and total (p = 0.002) QoL domains. There was a negative correlation between the DIGEST scale and the emotional domain of the QoL protocol (p = 0.045). The swallowing function proved to be relevant for QoL. Conclusion The PAS scale did not show any correlation with QoL. The functional performance of swallowing according to the DIGEST scale was coherent with the QOL scores. It is suggested that the residue may be a more relevant aspect for QoL than the aspiration, making DIGEST a promising tool in the assessment of dysphagic patients.

How Atoms of Polycrystalline Nb 20.6 Mo 21.7 Ta 15.6 W 21.1 V 21.0 refractory High-Entropy Alloys Rearrange during the Melting Process

The melting mechanism of single crystal and polycrystalline Nb 20.6 Mo 21.7 Ta 15.6 W 21.1 V 21.0 RHEAs was investigated by the molecular dynamics (MD) simulation using the 2NN MEAM potential. For the single crystal RHEA, the density profile displays an abrupt drop from 11.25 to 11.00 g/cm 3 at temperatures from 2910 to 2940 K, indicating all atoms begin significant local structural rearrangement. For polycrystalline RHEAs, a two-stage melting process is found. In the first melting stage, the melting of the grain boundary (GB) regions firstly occurs at the pre-melting temperature, which is relatively lower than the corresponding system-melting point. At the pre-melting temperature, most GB atoms have enough kinetic energies to leave their equilibrium positions, and then gradually induce the rearrangement of grain atoms close to GB. In the second melting stage at the melting point, most grain atoms have enough kinetic energies to rearrange, resulting in the chemical short-ranged order (CSRO) changes of all pairs.